7BXV | pdb_00007bxv

11A1 antibody-peptide complex

PDB DOI: https://doi.org/10.2210/pdb7BXV/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Mutation(s): No

Deposited: 2020-04-21 Released: 2021-04-21
Deposition Author(s): Irie, K., Irie, Y., Kita, A., Miki, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.194 (Depositor), 0.204 (DCC)
R-Value Work:
0.166 (Depositor), 0.174 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

APOE epsilon 4 allele advances the age-dependent decline of amyloid beta clearance in the human cortex.

Saito, A., Kageyama, Y., Pletnikova, O., Rudow, G.L., An, Y., Irie, Y., Kita, A., Miki, K., Li, L., Southall, P., Irie, K., Troncoso, J.C.

(2022) bioRxiv

DOI: https://doi.org/10.1101/2021.04.07.438832

Macromolecule Content

Total Structure Weight: 48.64 kDa
Atom Count: 3,816
Modeled Residue Count: 439
Deposited Residue Count: 440
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab of the 11A1 antibody L chain	A [auth L]	217	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab of the 11A1 antibody H chain	B [auth H]	218	Mus musculus	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TYR-GLU-VAL-HIS-HIS	C [auth A]	5	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H SDF format, chain G [auth H] SDF format, chain F [auth H] SDF format, chain E [auth L] SDF format, chain D [auth L] MOL2 format, chain H MOL2 format, chain G [auth H] MOL2 format, chain F [auth H] MOL2 format, chain E [auth L] MOL2 format, chain D [auth L] mmCIF format, chain H mmCIF format, chain G [auth H] mmCIF format, chain F [auth H] mmCIF format, chain E [auth L] mmCIF format, chain D [auth L]	D [auth L], E [auth L], F [auth H], G [auth H], H	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Interactions & Density Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth H] Focus chain G [auth H] Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.194 (Depositor), 0.204 (DCC)
R-Value Work: 0.166 (Depositor), 0.174 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.639	α = 90
b = 123.774	β = 99.743
c = 45.692	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19H00921

Revision History (Full details and data files)

Version 1.0: 2021-04-21
Type: Initial release
Version 1.1: 2022-05-04
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary